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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatcagcatcatagttttctacctgaggatcttgaaccgcaatcccttgtgtataataatatttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC

Basic information

species Oryza sativa
transcript LOC_Os01g17240.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G092793_T01 (Zea mays), 3'ss of exon 5
gtatgatcag-catcatagttttctacctgaggatcttgaaccgcaatcccttgtgtataataatatt----taaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC
|||  |  |  ||||| |  |||| |||||   ||| |||||    | |  | ||| || | ||  ||    | |||| |||||||||||||||||||||  ||||| |||||| |||||||||| |||||||| || ||||| |||||||||||| ||||||||||||| ||||| || |
gtaacactaaacatca-aactttcaacctggatatcatgaacttttaccattcgtgcattaaaaagttgctttgaaaatagGTTCTGAAATTCAACCTCATGGAATCTGGCCTTATCTGTGTTCTTCCCTGGTTCACCATGGCGGTTTCTGCAAATGTTGGTGGTTGGATTGCAGACACAC

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA18G07320.1 (Glycine max), 3'ss of exon 6
--------------gtatgatcagcatcatagttttc-----tacctgaggatc--ttga-accgcaatcccttgtgtataataatatttaaaaac--agGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC
                ||  |  |  || || | |||     ||  |||  | |  |||| || |       ||   || | | || || | | |   ||||  |||| || || || |||||||| || || || |||||| | || ||||| | ||||||  ||||||||||| ||||||||||||| ||||| || |
tatcctgacatacaaaatatttggattcgtaatcttcatggatatttgaaaaacaattgacactgtttaaaattaactaaagttattttcatatatctagGTCTTGAAGTTTAATCTTACAGAATCTGGGCTATTTTGTGTTTTACCATGGTTGATAATGGCTATTTCTGCAAATGTTGGTGGTTGGATTGCAGACACTC

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G26510.1 (Glycine max), 3'ss of exon 5
----------------gtatgatcagcatcatagttttct-----acctgaggatct-tgaaccgcaatcccttgtgtataataatatttaaaaac--agGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC
                  ||  |  |  |  |||| ||||     |  |||  | |  |  || |   |   ||   || | | || || | | |   ||||  |||| || || || |||||||| || || || |||||| | || ||||| | ||||||  ||||||||||| ||||||||||||| ||||| || |
aatatcctgacatacaaaatatttggatttgtagtcttcttggatatttgaaaaacaattgacagtgtttaattaactaaagttattttcatatatctagGTCTTGAAGTTTAATCTTACAGAATCTGGGCTATTTTGTGTTTTACCGTGGTTTATAATGGCTATTTCTGCAAATGTTGGTGGTTGGATTGCAGACACTC

upper sequence: LOC_Os01g17240.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0004g06220.t01 (Vitis vinifera), 3'ss of exon 5
--------gtatgatcagcatca--tagttttctacctgaggatcttgaaccgcaatcccttgtgtataataatat--ttaaaaac------------agGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC
           |  | |   |||  || | || |  ||  |  |  | ||  | |||   |||  |  ||| | ||  || ||  |            ||||| |||| ||||| || |||||||| || ||||| |||||  | |||||| | ||||||||  ||||||| ||| |||| || |||||||||||||| |
ttggctacagttctttaatttcaagtaatattttttcttggttttgttaaaagaaatattttgcctgcaatgagataattgaatgcggaatattttatagGTTTTGAAGTTCAATCTTACAGAATCTGGGCTTTTTTGTGTGTTGCCCTGGCTTACAATGGCGTTTTCTGCCAATCTTGGAGGGTGGATAGCAGATACAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58594059|gb|CF992367.1|CF992367
EST:     CTGGGGAACTTTCATCTTGCTCACATGGATGCCAACAGTAGTACAACCAG                         GTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
genomic: CTGGGGAACTTTCATCTTGCTCACATGGATGCCAACA-TACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
EST: gi|33679924|gb|CF308163.1|CF308163
EST:     TCATCTTGCTCACATGGATGCCAACATACTACAACCAG                         GTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
genomic: TCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
EST: gi|58689321|gb|CK078008.1|CK078008
EST:     ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAG                         GTTCTGAAATTCAACCTCACAGAATCCG
genomic: ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCG
EST: gi|24468687|gb|CA305636.1|CA305636
EST:     ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAG                         GTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
genomic: ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
EST: gi|58691317|gb|CK080004.1|CK080004
EST:     ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAG                         GTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
genomic: ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGG
EST: gi|218504692|gb|FG962736.1|FG962736
EST:     ACTGGGGAACTTTCATCTTGCTGACATGGATGCCAACATAGTACAAGCAG                         GTTGTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTGCCGCTG
genomic: ACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCC-CTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 58 (upstream exon), 74 (downstream exon)
Score: 40

ATTATCGAAACCCCCTGTTTGGGCTCTTATAGTGTCTCATTTCTGCCATAACTGGGGAACTTTCATCTTGCTCACATGGATGCCAACATACTACAACCAGgtatgatcag ... ttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacctgaggatcttgaaccgcaatcccttgtgtataataatatttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC
                             ttgtgtataataatat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatcagcatcatagttttctacctgaggatcttgaaccgcaatcccttgtgtataataatatttaaaaacagGTTCTGAAATTCAACCTCACAGAATCCGGCCTTTTCTGTGTTCTCCCCTGGTTAACAATGGCAGTTTCTGCAAATTTTGGTGGTTGGATAGCAGATACGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT